Eighteen years after a young boy stumbled on a pregnant woman’s raped and strangled body on a Harlem rooftop, her accused killer was hauled before a judge today — thanks to new testing of old forensics from the horrific slaying.

The murderer of Isabelle Joye, 32, of St. Nicholas Avenue, had left a tissue stained with his DNA nearby, and more of his DNA inside her body and under her fingernails. Now that genetic profile has been matched to imprisoned sex fiend Melvin Kelly, 55, prosecutors said.

At the time, in May of 1994, “Detectives investigated as best they could, but there were over 2,000 murders in New York City that year, and the case went cold,” the Manhattan DA’s Cold Case Unit chief, Melissa Mourges, told Manhattan Supreme Court Justice A. Kirke Bartley at a brief arraignment today.

The press — distracted at the time by the death of Jackie O — paid virtually no attention to the violent death of Joye, who was five months pregnant with an otherwise healthy baby boy when her body was found, stripped from the waist down and severely scraped from having been dragged across the tarpaper roof.

Still, the city medical examiner’s office kept hold of the tissue and swabs all these years, and earlier this year developed a male DNA profile that matched Kelly, Mourges said.

“Clearly she had fought and scratched him as he raped and strangled her,” the prosecutor said.

Kelly has been in prison for a 2004 sex assault on a 19-year-old man in Greenwich Village, and is serving a 25-to-life for first degree criminal sexual act and aggravated sex abuse, officials said.

“Now we have to make sure there is no contamination and everything was done properly,” court-appointed lawyer Glenn Abolafia said of the evidence that has come back to haunt his client.

Kelly pleaded not guilty to second degree murder and was hauled back to Elmira Correctional Facility; the judge set Jan. 31 as his next court date.